Next we study an atomistic, explicitly solvated model of Protein B, a much more complex system with 47 residues that was simulated using regular molecular dynamics for \(104\mu \) s, enough time to observe multiple folding/unfolding events [1]}.
As noted above, trajectories in a continuous space can be treated by a cluster-then-classify strategy applied in path space.
Here, however, we recapitulate the strategy used in the toy model of projecting configurations into a discrete space and using the fundamental-sequence analysis.
